Histone post-translational modifications are key epigenetic processes controlling the regulation of gene transcription. In recent years it has become apparent that chromatin modifications contribute to cognition through the modulation of gene expression required for the expression and consolidation of memories. In this review, we focus on the role of histone methylation in the nervous system. Histone methylation is involved in a number of cognitive disturbances, such as intellectual disability, cocaine addiction and age-related cognitive decline. We provide an overview of the dynamic changes in methylation of histone lysine residues during learning and memory. With a special focus on H3K9 histone methyltransferases GLP and G9a, we summarize the effects of deficiencies in writer and eraser enzymes on neuronal plasticity and cognition.